Detection of HPV

ABSTRACT

The present invention provides compositions and methods for the detection and characterization of HPV sequences. More particularly, the present invention provides compositions, methods and kits for using invasive cleavage structure assays (e.g. the INVADER assay) to screen nucleic acid samples, e.g., from patients, for the presence of any one of a collection of HPV sequences. The present invention also provides compositions, methods and kits for screening sets of HPV sequences in a single reaction container.

The present application is a Continuation of U.S. application Ser. No. 10/951,241, filed Sep. 27, 2004, which claims priority to U.S. Provisional Application Ser. No. 60/505,786, filed Sep. 25, 2003, both of which are herein incorporated by reference in their entireties.

FIELD OF THE INVENTION

The present invention provides methods and composition related to nucleic acid detection assays for use in basic research, clinical research, and for the development of clinical detection assays. In particular, the present invention provides methods for characterizing human papillomavirus (HPV) sequences.

BACKGROUND

Cervical cancer accounts for nearly 10% of all female cancers and is a leading cause of cancer among women in developing countries (Franco, E. L. et al., Can Med Assoc J. 2001; 164:1017-25). The regions with the highest incidence of the disease are generally those with the greatest mortality and include Central America, Africa, and the Carribean (Ferlay, J. et al., 1998. IARC CancerBase no. 3. Lyon:IARCPress.). Incidence in Europe and North America has declined precipitously over the past 50 years, possibly due to the advent of routine screening by Papanicolaou (Pap) smear testing (reviewed in Franco et al., ibid). Cervical cancer is one of the most preventable cancers, with survival being directly related to the stage of the disease at diagnosis. The 5-year survival rate is 88% for women having initial diagnosis of localized disease as opposed to 13% for women diagnosed with distant disease (Report of the Gynecologic Cancers Progress Review Group, November 2001, National Cancer Institute). More than 50% of women diagnosed with cervical cancer in the U.S. have not had a Pap smear in the past three years (Wright, T. C. et al., JAMA. 2000; 283:81-6).

Pap screening remains the predominant mode of detecting cancerous and precancerous cervical lesions; more than 50 million women undergo Pap screening each year in the U.S. (Wright, T. C. et al., JAMA 2002; 287:2120-29). Despite its widespread use, Pap smear testing is only partially effective; some estimates place the sensitivity of conventional Pap smear testing at 50-60% (Lorincz, A. T. and Richart, R. M., (Arch Pathol Lab Med. 2003; 127:959-68; Nanda, K. et al., 2000. Ann Intern Med 132:810.; Fahey M T, et al. Am J Epidemiol. 1995; 141:680-9; Myers E R, McCrory D C, Subramanian S, et al. Obstet Gynecol. 2000; 96:645-52.) or 70-80% (Clavel, C. et al., 2001. Br J Cancer 84:1616). Recent innovations in cytological screening and sampling, such as liquid-based tests, have improved the sensitivity of these methods to 75-95% (Lorincz, A. T. et al. ibid; Nanda, K. et al., ibid.; Hutchinson M L, Zahniser D J, Sherman M E, et al. Cancer. 1999; 87:48-55.). Nonetheless, even these improved methods fail to detect a significant portion of abnormal, and often precancerous, cells. Once identified, patients with atypical squamous cells of undetermined significance (ASCUS) are subjected to various levels of monitoring and treatment, depending on the particular attendant risk factors and clinical presentation (reviewed in Wright, T. C. et al. JAMA 2002, ibid).

Human Papillomavirus (HPV) has been identified as the primary, and possibly only, cause of cervical cancer (Muñoz N, Bosch F X, de Sanjosé S, et al., Int J Cancer 1992; 52:743-9; Bosch F X, Lorincz A, Munoz N, Meijer Shah K V., Clin Pathol 2002; 55:244-65), implicated in as many as 99.7% of all cases (Wallboomers, J. M. et al., 1999. J Pathol 189:12-19). The HPV genome is an 8 kb, circular, double stranded DNA comprising 8 genes, all encoded on the same strand. As many as 200 different HPV types have been identified in humans (Burd, E. M. Clin Microbiol Rev. 2003; 16:1-17); of these approximately 40 types have been found capable of infecting the genital tract (Munoz, N. N Engl J Med 2003; 348:518-27.). Still further classification has resulted in the identification of high- and low-risk viral types for development of cervical cancer. Estimates place the number of high-risk types between 13-19 strains, with two strains, HPV 16 and 18 together accounting for as much as 55-85% of infections, depending on subject age and geographical location (Munoz, N., ibid). The predominant low-risk strains are HPV 6 and 11; these may lead to genital warts (reviewed in Burd, E. M., ibid).

The elucidation of certain high risk HPV strains as the causative agents of cervical cancer, coupled with advances in molecular biological methods, has expanded the spectrum of methods available for both preventing and detecting HPV infection. Vaccines for the most common high-risk HPV strains are currently in clinical trials (Koutsky, L A. et al., 2002. NEJM 347:1645-51). Moreover, some authorities are calling for HPV DNA screening for use in conjunction with, or in some cases, in lieu of, conventional cytological methods (Wright, T. C. and Schiffman, M. N. Engl. J. Med, 2003; 348: 489-90). Various alternative DNA-based detection methods have been introduced, including the HYBRID CAPTURE II (HCII) test (Digene, Gaithersburg, Md.), which was been approved by the FDA in March, 1999. The HYBRID CAPTURE method relies on hybridization of target DNA to complementary RNA probes. The resultant RNA-DNA hybrids are recognized by surface-bound antibodies as well as antibodies conjugated to alkaline phosphatase, allowing generation of a chemiluminescent signal in the presence of appropriate substrates (Lorincz, A. T. J Obstet Gynaecol Res. 1996; 22:629-36; also U.S. Pat. No. 4,908,306 and related patents and applications). Further alternative methods include the use of sequence specific probes for use in PCR or sandwich hybridization assays, such as those described in U.S. Pat. No. 6,583,278. Other methods rely on various PCR primers for selective amplification of specific strains, as in U.S. Pat. No. 5,447,839 and related applications. Still other methods rely on in situ hybridization of sequence-specific probes to isolated cervical cells, described in WO 00/24760A1 (e.g. INFORM HPV, Ventana Medical Systems, Inc., Tuscon, Ariz.; Qureshi M N et al., Diagn. Cytopathol. 2003; 29:149-155).

Therefore, there exists a need for a rapid, sensitive, and highly quantitative direct detection assay for detecting HPV infection by high risk strains in cervical samples. Given the current reliance on molecular methods, it is likely that there will be an ongoing and increasing need for rapid, quantitative methods of detecting HPV infection.

SUMMARY OF THE INVENTION

The present invention provides compositions and methods for the detection and characterization of sequences associated with human papillomavirus (HPV). More particularly, the present invention provides compositions, methods and kits for using invasive cleavage structure assays (e.g. the INVADER assay, Third Wave Technologies, Madison, Wis.) to screen nucleic acid samples, e.g., from patients, for the presence of any one or more of a collection of sequences associated with HPV. The present invention also provides compositions, methods and kits for screening sets of different HPV sequences in a single reaction container. The present invention may be used to detect integrated and/or non-integrated viral sequences.

In other embodiments, synthetic DNA suitable for use with the methods and compositions of the present invention is made using a purified polymerase on multiply-primed genomic DNA, as provided, e.g., in U.S. Pat. Nos. 6,291,187, and 6,323,009, and in PCT applications WO 01/88190 and WO 02/00934, each herein incorporated by reference in their entireties for all purposes. In these embodiments, amplification of DNA such as genomic DNA is accomplished using a DNA polymerase, such as the highly processive Φ29 polymerase (as described, e.g., in U.S. Pat. Nos. 5,198,543 and 5,001,050, each herein incorporated by reference in their entireties for all purposes) in combination with exonuclease-resistant random primers, such as hexamers.

The method is not limited by the nature of the target nucleic acid. In some embodiments, the target nucleic acid is single stranded or double stranded DNA or RNA. In some embodiments, double stranded nucleic acid is rendered single stranded (e.g., by heat) prior to formation of the cleavage structure. In some embodiments, the source of target nucleic acid comprises a sample containing genomic DNA. Sample include, but are not limited to, tissue sections, blood, saliva, cerebral spinal fluid, pleural fluid, milk, lymph, sputum and semen.

In some embodiments, the present invention provides methods of detecting an HPV sequence or method for diagnosing cancer, comprising; a) providing; i) a sample from a subject; and ii) a composition comprising an oligonucleotide detection assay (e.g. as described herein); and b) contacting said sample with said composition such that the presence or absence of at least one HPV sequence is determined. In some embodiments, the sample is a tissue section, blood sample, mouth swab sample, saliva sample, or other biological fluid sample from the subject.

In some embodiments, the present invention provides a method for detecting at least one HPV sequence in a sample, comprising using a first and a second oligonucleotide, wherein the oligonucleotides are configured to form an invasive cleavage structure with a target sequence comprising the at least one HPV sequence. In some embodiments, the first oligonucleotide comprises a 5′ portion and a 3′ portion, wherein the 3′ portion is configured to hybridize to the target sequence, and the 5′ portion is configured to not hybridize to the target sequence. In some embodiments, the second oligonucleotide comprises a 5′ portion and a 3′ portion, wherein the 5′ portion is configured to hybridize to the target sequence, and wherein the 3′ portion is configured to not hybridize to the target sequence. In preferred embodiments, the first and second oligonucleotides are selected from the group consisting of SEQ ID NOS. 1-5, 7-62, 64-67, 69-70, 73-116 and 122-193.

In some embodiments, the present invention provides a method for detecting the presence or absence of HPV nucleic acid in a sample comprising providing a sample comprising nucleic acids and an invasive cleavage assay configured to detect at least one HPV nucleic acid and exposing the sample to the detection assay under conditions such that the at least one HPV nucleic acid can be detected, and detecting the presence or absence of HPV nucleic acid in a sample. In some embodiments, the detecting comprises identifying one or more strains of HPV present in the sample. In preferred embodiments, the HPV strain is selected from the group consisting of, but not limited to, HPV 16, 16Ty2, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 58iso, 59, 66, 67, 68, 68var, 69, 70, or 82. In some embodiments, the nucleic acid is amplified prior to said exposure step.

In some embodiments, the present invention provides a method for detecting the presence or absence of HPV nucleic acid in a sample comprising treating the sample using a first oligonucleotide and a second oligonucleotide, wherein the oligonucleotides are configured to form an invasive cleavage reaction and detecting the presence or absence of HPV nucleic acid. In particular embodiments, the oligonucleotides comprise one or more oligonucleotides selected from the group consisting of, but not limited to, SEQ ID NOS. 1-5, 7-62, 64-67, 69-70, 73-116 and 122-193. In some preferred embodiments, the oligonucleotides individually contain one or more mismatches with target HPV nucleic acid. In some embodiments, the oligonucleotides are configured to hybridize to non-HPV nucleic acid sequences or two hybridize to two or more strains of HPV. In some embodiments, the oligonucleotides are configured such that a stable hybridization duplex between one or more of the oligonucleotides and the HPV target nucleic acid is not formed.

In some embodiments, the target nucleic acid comprises genomic DNA or mRNA. In other embodiments, the target nucleic acid comprises synthetic DNA or RNA. In some preferred embodiments, synthetic DNA or RNA within a sample is created using a purified polymerase. In some preferred embodiments, creation of synthetic DNA using a purified polymerase comprises the use of PCR. In some preferred embodiments, creation of synthetic DNA comprises use of the methods and compositions for amplification using RNA-DNA composite primers (e.g., as disclosed in U.S. Pat. No. 6,251,639, herein incorporated by reference in its entirety). In other preferred embodiments, creation of synthetic DNA using a purified DNA polymerase suitable for use with the methods of the present invention comprises use of rolling circle amplification, (e.g., as in U.S. Pat. Nos. 6,210,884, 6,183,960 and 6,235,502, herein incorporated by reference in their entireties). In other preferred embodiments, creation of synthetic DNA comprises amplification using nucleic acids comprising loop-forming sequences, e.g., as described in U.S. Pat. No. 6,410,278, herein incorporated by reference in its entirety.

In some embodiments, the present invention provides methods and kits configured to detect more than one HPV strain in a single reaction vessel (e.g., kits and methods to detect all high risk strains in four or fewer reactions). Thus, the present invention provides kits and methods comprising pooled detection assay components. In some preferred embodiments, a single oligonucleotide in the pooled detection assay components is configured to take part in an invasive cleavage structure in the presence of two or more HPV target strains. The pooled detection assay components also find use in methods and kits using detection technologies other than invasive cleavage technology. For example, the pooled detection assays for detection of HPV sequences (e.g., wherein one or more oligonucleotides find use in detecting multiple HPV sequences in a single reaction) provided in the present invention may find use in detection assays that include, but are not limited to, enzyme mismatch cleavage methods (e.g., Variagenics, U.S. Pat. Nos. 6,110,684, 5,958,692, 5,851,770, herein incorporated by reference in their entireties); polymerase chain reaction; branched hybridization methods (e.g., Chiron, U.S. Pat. Nos. 5,849,481, 5,710,264, 5,124,246, and 5,624,802, herein incorporated by reference in their entireties); rolling circle replication (e.g., U.S. Pat. Nos. 6,210,884, 6,183,960 and 6,235,502, herein incorporated by reference in their entireties); NASBA (e.g., U.S. Pat. No. 5,409,818, herein incorporated by reference in its entirety); molecular beacon technology (e.g., U.S. Pat. No. 6,150,097, herein incorporated by reference in its entirety); E-sensor technology (Motorola, U.S. Pat. Nos. 6,248,229, 6,221,583, 6,013,170, and 6,063,573, herein incorporated by reference in their entireties); cycling probe technology (e.g., U.S. Pat. Nos. 5,403,711, 5,011,769, and 5,660,988, herein incorporated by reference in their entireties); Dade Behring signal amplification methods (e.g., U.S. Pat. Nos. 6,121,001, 6,110,677, 5,914,230, 5,882,867, and 5,792,614, herein incorporated by reference in their entireties); ligase chain reaction (Barnay Proc. Natl. Acad. Sci USA 88, 189-93 (1991)); and sandwich hybridization methods (e.g., U.S. Pat. No. 5,288,609, herein incorporated by reference in its entirety).

In some embodiments, the present invention provides kits or compositions comprising a non-amplified oligonucleotide detection assay configured for detecting at least one HPV sequence. In other embodiments, the non-amplified oligonucleotide detection assay comprises first and second oligonucleotides configured to form an invasive cleavage structure (e.g. an INVADER assay) in combination with a target sequence comprising said at least one HPV sequence. In particular embodiments, the first oligonucleotide comprises a 5′ portion and a 3′ portion, wherein the 3′ portion is configured to hybridize to the target sequence, and wherein the 5′ portion is configured to not hybridize to the target sequence. In other embodiments, the second oligonucleotide comprises a 5′ portion and a 3′ portion, wherein the 5′ portion is configured to hybridize to the target sequence, and wherein the 3′ portion is configured to not hybridize to the target sequence.

In some embodiments, the present invention provides a kit comprising oligonucleotide detection assays configured for detecting a HPV sequence, wherein the kit comprises one or more oligonucleotides selected from the group consisting of SEQ ID NOS. 1-193. In particular embodiments, the multiple HPV strains are detected simultaneously by combining one or more of the oligonucleotides into one or more reactions. In preferred embodiments, none of the oligonucleotides are completely complementary to HPV target nucleic acid sequences. In some embodiments, the oligonucleotides comprise sequences not completely complementary to any target sequence that is detected. In preferred embodiments, all high-risk HPV strains are detected in four or fewer reactions. In other preferred embodiments, all high-risk HPV strains can be detected in three or fewer reactions.

In some embodiments, the present invention provides a kit comprising oligonucleotide detection assays configured for detecting all high-risk HPV strains. In preferred embodiments, the oligonucleotides are not fully complementary to nucleic acid sequences of the HPV strains. In further preferred embodiments, the oligonucleotides hybridize to multiples regions of a single HPV nucleic acid (e.g., to provide redundancy in detection). In even further preferred embodiments, the oligonucleotides are selected from the group consisting of SEQ ID NOS. 77-116 and 122-193.

In some embodiments, the detected HPV sequences are any of those found below in Table 1 or variants thereof. It is understood that sequences will diverge over time and that other HPV varieties, now know, or later discovered are readily adaptable to the methods and composition of the present invention, per the description herein.

TABLE 1 strain accession  1a NC_001356  1a U06714  2a X55964  3 NC_001588  3 X74462  4 NC_001457  4 X70827  5 M17463  5 NC_001531  5b D90252  5b NC_001444  6a L41216  6a NC_001668  6b NC_001355  6 AF092932  6 NC_000904  7 M12588  7 NC_001595  7 X74463  8 M12737  8 NC_001532  9 NC_001596  9 X74464 10 NC_001576 10 X74465 11 J04351 11 M14119 11 NC_001525 12 NC_001577 12 X74466 13 NC_001349 13 X62843 14d NC_001578 14d X74467 15 NC_001579 15 X74468 16 AF125673 16 AF472508 16 AF472509 16 K02718 16 NC_001526 16 U89348 17 NC_001580 17 X74469 18 NC_001357 18 X05015 18 X05349 19 NC_001581 19 X74470 20 NC_001679 20 U31778 21 NC_001680 21 U31779 22 NC_001681 22 U31780 23 NC_001682 23 U31781 24 NC_001683 24 U31782 25 NC_001582 25 X74471 26 NC_001583 26 X74472 27 NC_001584 27 X74473 28 NC_001684 28 U31783 29 NC_001685 29 U31784 30 NC_001585 30 X74474 31 J04353 31 NC_001527 32 NC_001586 32 X74475 33 M12732 33 NC_001528 34 NC_001587 34 X74476 35 M74117 35 NC_001529 35h X74477 36 NC_001686 36 U31785 37 NC_001687 37 U31786 38 NC_001688 38 U31787 39 M62849 39 AF548856 39 AF548857 39 NC_001535 40 NC_001589 40 X74478 41 NC_001354 41 X56147 42 NC_001534 42 M73236 43 U12504 43 Y12214 44 NC_001689 44 U31788 45 NC_001590 45 X74479 47 M32305 47 NC_001530 48 NC_001690 48 U31789 49 NC_001591 49 X74480 50 NC_001691 50 U31790 51 M62877 51 NC_001533 52 NC_001592 52 X74481 53 NC_001593 53 X74482 54 AF436129 54 NC_001676 54 U37488 55 NC_001692 55 U31791 56 NC_001594 56 X74483 57 NC_001353 57 X55965 57b U37537 58 D90400 58 NC_001443 59 NC_001635 59 X77858 60 NC_001693 60 U31792 61 NC_001694 61 U31793 62 U12499 63 NC_001458 63 X70828 64 U12495 65 NC_001459 65 X70829 66 NC_001695 66 U31794 67 D21208 68 M73258 68 Y14591 69 AB027020 69 NC_002171 70 NC_001711 70 U21941 71 AB040456 71 NC_002644 72 X94164 73 X94165 74 AF436130 74 NC_004501 75 Y15173 76 Y15174 77 Y15175 80 Y15176 82 AB027021 82 AF293961 82 NC_002172 83 AF151983 83 NC_000856 84 AF293960 84 NC_002676 85 AF131950 86 AF349909 86 NC_003115 87 AJ400628 87 NC_002627 89 NC_004103 90 AY057438 90 NC_004104 91 AF419318 91 AF436128 91 NC_004085 92 AF531420 92 NC_004500 RXRX7 U85660

In certain embodiments, the oligonucleotide detection assays are selected from sequencing assays, polymerase chain reaction assays, hybridization assays, hybridization assays employing a probe complementary to a mutation, microarray assays, bead array assays, primer extension assays, enzyme mismatch cleavage assays, branched hybridization assays, rolling circle replication assays, NASBA assays, molecular beacon assays, cycling probe assays, ligase chain reaction assays, invasive cleavage structure assays, ARMS assays, and sandwich hybridization assays.

The present invention also provides methods of detecting target nucleic acids through the use of probe sequences that are not completely complementary to the target nucleic acid. For example, the present invention provides kits and methods for detecting a target sequence by using mismatch probe sequences, comprising the steps of: a) providing a sample suspected of containing a target nucleic acid; b) exposing the sample to one or more oligonucleotides that contain a region that is complementary to said target nucleic acid, said region having a first portion completely complementary to said target nucleic acid, a second portion contiguous to said first portion that is not complementary to said target nucleic acid (e.g., a mismatch), and a third portion contiguous to said second portion that is completely complementary to the target nucleic acid; and c) detecting the target nucleic acid under conditions such that no sequences that are completely complementary to the one or more oligonucleotides or said region of the one or more oligonucleotides are detected (i.e., only sequences that are not completely complementary to the oligonucleotides or the region of the oligonucleotides are detected). Thus, even if the sample contains perfect complements to the oligonucleotides or to the region, such perfect complements are not detected. This can be carried out, for example, through use of two or more oligonucleotides that, through their coordinated action, provide specificity for the non-matched target sequence, but do not detect the perfect complement. The INVADER assay, methods employing ligation, the polymerase chain reaction, etc. are examples of methods that permit such detection. This can also be carried out with a single probe sequence in a hybridization method if the probe is of sufficient length to ensure that it is not completely complementary to any sequence in the sample that might be detected.

In some embodiments, the region of the one or more oligonucleotides contains two or more mismatches to the target nucleic acid (e.g., 3, 4, 5, 6, . . . ). In some embodiments, the region contains no more than twenty (e.g., no more than 15, 12, 10, 9, 8, 7, 6, . . . ) contiguous nucleotides that are completely complementary to the target nucleic acid. In some embodiments, one or more of the oligonucleotides are generated by extending a primer in an enzymatic extension reaction using the target nucleic acid as a template (e.g., in a polymerase chain reaction). In some embodiments, the target nucleic acid is a viral target nucleic acid (e.g., HPV). In some embodiments, the target nucleic acid is a conserved region of a viral genome (i.e., a region that is highly conserved between different strains or family members of the virus). For example, the LCR, E6, and E7 regions of the HPV genome contain conserved sequences.

DEFINITIONS

To facilitate an understanding of the present invention, a number of terms and phrases are defined below:

As used herein, the terms “subject” and “patient” refer to any organisms including plants, microorganisms and animals (e.g., mammals such as dogs, cats, livestock, and humans).

As used herein, the term “INVADER assay reagents” refers to one or more reagents for detecting target sequences, said reagents comprising oligonucleotides capable of forming an invasive cleavage structure in the presence of the target sequence. In some embodiments, the INVADER assay reagents further comprise an agent for detecting the presence of an invasive cleavage structure (e.g., a cleavage agent). In some embodiments, the oligonucleotides comprise first and second oligonucleotides, said first oligonucleotide comprising a 5′ portion complementary to a first region of the target nucleic acid and said second oligonucleotide comprising a 3′ portion and a 5′ portion, said 5′ portion complementary to a second region of the target nucleic acid downstream of and contiguous to the first portion. In some embodiments, the 3′ portion of the second oligonucleotide comprises a 3′ terminal nucleotide not complementary to the target nucleic acid. In preferred embodiments, the 3′ portion of the second oligonucleotide consists of a single nucleotide not complementary to the target nucleic acid.

In some embodiments, INVADER assay reagents are configured to detect a target nucleic acid sequence comprising first and second non-contiguous single-stranded regions separated by an intervening region comprising a double-stranded region. In preferred embodiments, the INVADER assay reagents comprise a bridging oligonucleotide capable of binding to said first and second non-contiguous single-stranded regions of a target nucleic acid sequence. In particularly preferred embodiments, either or both of said first or said second oligonucleotides of said INVADER assay reagents are bridging oligonucleotides.

In some embodiments, the INVADER assay reagents further comprise a solid support. For example, in some embodiments, the one or more oligonucleotides of the assay reagents (e.g., first and/or second oligonucleotide, whether bridging or non-bridging) is attached to said solid support. In some embodiments, the INVADER assay reagents further comprise a buffer solution. In some preferred embodiments, the buffer solution comprises a source of divalent cations (e.g., Mn²⁺ and/or Mg²⁺ ions). Individual ingredients (e.g., oligonucleotides, enzymes, buffers, target nucleic acids) that collectively make up INVADER assay reagents are termed “INVADER assay reagent components.”

In some embodiments, the INVADER assay reagents further comprise a third oligonucleotide complementary to a third portion of the target nucleic acid upstream of the first portion of the first target nucleic acid. In yet other embodiments, the INVADER assay reagents further comprise a target nucleic acid. In some embodiments, the INVADER assay reagents further comprise a second target nucleic acid. In yet other embodiments, the INVADER assay reagents further comprise a third oligonucleotide comprising a 5′ portion complementary to a first region of the second target nucleic acid. In some specific embodiments, the 3′ portion of the third oligonucleotide is covalently linked to the second target nucleic acid. In other specific embodiments, the second target nucleic acid further comprises a 5′ portion, wherein the 5′ portion of the second target nucleic acid is the third oligonucleotide. In still other embodiments, the INVADER assay reagents further comprise an ARRESTOR molecule (e.g., ARRESTOR oligonucleotide).

In some preferred embodiments, the INVADER assay reagents further comprise reagents for detecting a nucleic acid cleavage product. In some embodiments, one or more oligonucleotides in the INVADER assay reagents comprise a label. In some preferred embodiments, said first oligonucleotide comprises a label. In other preferred embodiments, said third oligonucleotide comprises a label. In particularly preferred embodiments, the reagents comprise a first and/or a third oligonucleotide labeled with moieties that produce a fluorescence resonance energy transfer (FRET) effect.

In some embodiments one or more the INVADER assay reagents may be provided in a predispensed format (i.e., premeasured for use in a step of the procedure without re-measurement or re-dispensing). In some embodiments, selected INVADER assay reagent components are mixed and predispensed together. In preferred embodiments, predispensed assay reagent components are predispensed and are provided in a reaction vessel (including but not limited to a reaction tube or a well, as in, e.g., a microtiter plate). In particularly preferred embodiments, predispensed INVADER assay reagent components are dried down (e.g., desiccated or lyophilized) in a reaction vessel.

In some embodiments, the INVADER assay reagents are provided as a kit. As used herein, the term “kit” refers to any delivery system for delivering materials. In the context of reaction assays, such delivery systems include systems that allow for the storage, transport, or delivery of reaction reagents (e.g., oligonucleotides, enzymes, etc. in the appropriate containers) and/or supporting materials (e.g., buffers, written instructions for performing the assay etc.) from one location to another. For example, kits include one or more enclosures (e.g., boxes) containing the relevant reaction reagents and/or supporting materials. As used herein, the term “fragmented kit” refers to delivery systems comprising two or more separate containers that each contains a subportion of the total kit components. The containers may be delivered to the intended recipient together or separately. For example, a first container may contain an enzyme for use in an assay, while a second container contains oligonucleotides. The term “fragmented kit” is intended to encompass kits containing Analyte specific reagents (ASR's) regulated under section 520(e) of the Federal Food, Drug, and Cosmetic Act, but are not limited thereto. Indeed, any delivery system comprising two or more separate containers that each contains a subportion of the total kit components are included in the term “fragmented kit.” In contrast, a “combined kit” refers to a delivery system containing all of the components of a reaction assay in a single container (e.g., in a single box housing each of the desired components). The term “kit” includes both fragmented and combined kits.

In some embodiments, the present invention provides INVADER assay reagent kits comprising one or more of the components necessary for practicing the present invention. For example, the present invention provides kits for storing or delivering the enzymes and/or the reaction components necessary to practice an INVADER assay. The kit may include any and all components necessary or desired for assays including, but not limited to, the reagents themselves, buffers, control reagents (e.g., tissue samples, positive and negative control target oligonucleotides, etc.), solid supports, labels, written and/or pictorial instructions and product information, software (e.g., for collecting and analyzing data), inhibitors, labeling and/or detection reagents, package environmental controls (e.g., ice, desiccants, etc.), and the like. In some embodiments, the kits provide a sub-set of the required components, wherein it is expected that the user will supply the remaining components. In some embodiments, the kits comprise two or more separate containers wherein each container houses a subset of the components to be delivered. For example, a first container (e.g., box) may contain an enzyme (e.g., structure specific cleavage enzyme in a suitable storage buffer and container), while a second box may contain oligonucleotides (e.g., INVADER oligonucleotides, probe oligonucleotides, control target oligonucleotides, etc.).

The term “label” as used herein refers to any atom or molecule that can be used to provide a detectable (preferably quantifiable) effect, and that can be attached to a nucleic acid or protein. Labels include but are not limited to dyes; radiolabels such as ³²P; binding moieties such as biotin; haptens such as digoxgenin; luminogenic, phosphorescent or fluorogenic moieties; mass tags; and fluorescent dyes alone or in combination with moieties that can suppress or shift emission spectra by fluorescence resonance energy transfer (FRET). Labels may provide signals detectable by fluorescence, radioactivity, colorimetry, gravimetry, X-ray diffraction or absorption, magnetism, enzymatic activity, characteristics of mass or behavior affected by mass (e.g., MALDI time-of-flight mass spectrometry), and the like. A label may be a charged moiety (positive or negative charge) or alternatively, may be charge neutral. Labels can include or consist of nucleic acid or protein sequence, so long as the sequence comprising the label is detectable.

As used herein, the term “distinct” in reference to signals refers to signals that can be differentiated one from another, e.g., by spectral properties such as fluorescence emission wavelength, color, absorbance, mass, size, fluorescence polarization properties, charge, etc., or by capability of interaction with another moiety, such as with a chemical reagent, an enzyme, an antibody, etc.

As used herein, the terms “complementary” or “complementarity” are used in reference to polynucleotides (i.e., a sequence of nucleotides such as an oligonucleotide or a target nucleic acid) related by the base-pairing rules. For example, for the sequence “5′-A-G-T-3′,” is complementary to the sequence “3′-T-C-A-5′.” Complementarity may be “partial,” in which only some of the nucleic acids' bases are matched according to the base pairing rules. Or, there may be “complete” or “total” complementarity between the nucleic acids. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands. This is of particular importance in amplification reactions, as well as detection methods that depend upon binding between nucleic acids. Either term may also be used in reference to individual nucleotides, especially within the context of polynucleotides. For example, a particular nucleotide within an oligonucleotide may be noted for its complementarity, or lack thereof, to a nucleotide within another nucleic acid strand, in contrast or comparison to the complementarity between the rest of the oligonucleotide and the nucleic acid strand.

The term “homology” and “homologous” refers to a degree of identity. There may be partial homology or complete homology. A partially homologous sequence is one that is less than 100% identical to another sequence.

As used herein, the term “hybridization” is used in reference to the pairing of complementary nucleic acids. Hybridization and the strength of hybridization (i.e., the strength of the association between the nucleic acids) is influenced by such factors as the degree of complementary between the nucleic acids, stringency of the conditions involved, and the T_(m) of the formed hybrid. “Hybridization” methods involve the annealing of one nucleic acid to another, complementary nucleic acid, i.e., a nucleic acid having a complementary nucleotide sequence. The ability of two polymers of nucleic acid containing complementary sequences to find each other and anneal through base pairing interaction is a well-recognized phenomenon. The initial observations of the “hybridization” process by Marmur and Lane, Proc. Natl. Acad. Sci. USA 46:453 (1960) and Doty et al., Proc. Natl. Acad. Sci. USA 46:461 (1960) have been followed by the refinement of this process into an essential tool of modern biology.

The complement of a nucleic acid sequence as used herein refers to an oligonucleotide which, when aligned with the nucleic acid sequence such that the 5′ end of one sequence is paired with the 3′ end of the other, is in “antiparallel association.” Certain bases not commonly found in natural nucleic acids may be included in the nucleic acids of the present invention and include, for example, inosine and 7-deazaguanine. Complementarity need not be perfect; stable duplexes may contain mismatched base pairs or unmatched bases. Those skilled in the art of nucleic acid technology can determine duplex stability empirically considering a number of variables including, for example, the length of the oligonucleotide, base composition and sequence of the oligonucleotide, ionic strength and incidence of mismatched base pairs.

As used herein, the term “T_(m)” is used in reference to the “melting temperature.” The melting temperature is the temperature at which a population of double-stranded nucleic acid molecules becomes half dissociated into single strands. Several equations for calculating the T_(m) of nucleic acids are well known in the art. As indicated by standard references, a simple estimate of the T_(m) value may be calculated by the equation: T_(m)=81.5+0.41 (% G+C), when a nucleic acid is in aqueous solution at 1 M NaCl (see e.g., Anderson and Young, Quantitative Filter Hybridization, in Nucleic Acid Hybridization (1985). Other references (e.g., Allawi, H. T. & SantaLucia, J., Jr. Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry 36, 10581-94 (1997) include more sophisticated computations which take structural and environmental, as well as sequence characteristics into account for the calculation of T_(m).

The term “gene” refers to a DNA sequence that comprises control and coding sequences necessary for the production of an RNA having a non-coding function (e.g., a ribosomal or transfer RNA), a polypeptide or a precursor. The RNA or polypeptide can be encoded by a full length coding sequence or by any portion of the coding sequence so long as the desired activity or function is retained.

The term “wild-type” refers to a gene or a gene product that has the characteristics of that gene or gene product when isolated from a naturally occurring source. A wild-type gene is that which is most frequently observed in a population and is thus arbitrarily designated the “normal” or “wild-type” form of the gene. In contrast, the term “modified”, “mutant” or “polymorphic” refers to a gene or gene product which displays modifications in sequence and or functional properties (i.e., altered characteristics) when compared to the wild-type gene or gene product. It is noted that naturally-occurring mutants can be isolated; these are identified by the fact that they have altered characteristics when compared to the wild-type gene or gene product.

The term “recombinant DNA vector” as used herein refers to DNA sequences containing a desired heterologous sequence. For example, although the term is not limited to the use of expressed sequences or sequences that encode an expression product, in some embodiments, the heterologous sequence is a coding sequence and appropriate DNA sequences necessary for either the replication of the coding sequence in a host organism, or the expression of the operably linked coding sequence in a particular host organism. DNA sequences necessary for expression in prokaryotes include a promoter, optionally an operator sequence, a ribosome binding site and possibly other sequences. Eukaryotic cells are known to utilize promoters, polyadenlyation signals and enhancers.

The term “oligonucleotide” as used herein is defined as a molecule comprising two or more deoxyribonucleotides or ribonucleotides, preferably at least 5 nucleotides, more preferably at least about 10-15 nucleotides and more preferably at least about 15 to 30 nucleotides. The exact size will depend on many factors, which in turn depend on the ultimate function or use of the oligonucleotide. The oligonucleotide may be generated in any manner, including chemical synthesis, DNA replication, reverse transcription, PCR, or a combination thereof. In some embodiments, oligonucleotides that form invasive cleavage structures are generated in a reaction (e.g., by extension of a primer in an enzymatic extension reaction).

Because mononucleotides are reacted to make oligonucleotides in a manner such that the 5′ phosphate of one mononucleotide pentose ring is attached to the 3′ oxygen of its neighbor in one direction via a phosphodiester linkage, an end of an oligonucleotide is referred to as the “5′ end” if its 5′ phosphate is not linked to the 3′ oxygen of a mononucleotide pentose ring and as the “3′ end” if its 3′ oxygen is not linked to a 5′ phosphate of a subsequent mononucleotide pentose ring. As used herein, a nucleic acid sequence, even if internal to a larger oligonucleotide, also may be said to have 5′ and 3′ ends. A first region along a nucleic acid strand is said to be upstream of another region if the 3′ end of the first region is before the 5′ end of the second region when moving along a strand of nucleic acid in a 5′ to 3′ direction.

When two different, non-overlapping oligonucleotides anneal to different regions of the same linear complementary nucleic acid sequence, and the 3′ end of one oligonucleotide points towards the 5′ end of the other, the former may be called the “upstream” oligonucleotide and the latter the “downstream” oligonucleotide. Similarly, when two overlapping oligonucleotides are hybridized to the same linear complementary nucleic acid sequence, with the first oligonucleotide positioned such that its 5′ end is upstream of the 5′ end of the second oligonucleotide, and the 3′ end of the first oligonucleotide is upstream of the 3′ end of the second oligonucleotide, the first oligonucleotide may be called the “upstream” oligonucleotide and the second oligonucleotide may be called the “downstream” oligonucleotide.

The term “primer” refers to an oligonucleotide that is capable of acting as a point of initiation of synthesis when placed under conditions in which primer extension is initiated. An oligonucleotide “primer” may occur naturally, as in a purified restriction digest or may be produced synthetically.

A primer is selected to be “substantially” complementary to a strand of specific sequence of the template. A primer must be sufficiently complementary to hybridize with a template strand for primer elongation to occur. A primer sequence need not reflect the exact sequence of the template. For example, a non-complementary nucleotide fragment may be attached to the 5′ end of the primer, with the remainder of the primer sequence being substantially complementary to the strand. Non-complementary bases or longer sequences can be interspersed into the primer, provided that the primer sequence has sufficient complementarity with the sequence of the template to hybridize and thereby form a template primer complex for synthesis of the extension product of the primer.

The term “cleavage structure” as used herein, refers to a structure that is formed by the interaction of at least one probe oligonucleotide and a target nucleic acid, forming a structure comprising a duplex, the resulting structure being cleavable by a cleavage means, including but not limited to an enzyme. The cleavage structure is a substrate for specific cleavage by the cleavage means in contrast to a nucleic acid molecule that is a substrate for non-specific cleavage by agents such as phosphodiesterases which cleave nucleic acid molecules without regard to secondary structure (i.e., no formation of a duplexed structure is required).

The term “cleavage means” or “cleavage agent” as used herein refers to any means that is capable of cleaving a cleavage structure, including but not limited to enzymes. “Structure-specific nucleases” or “structure-specific enzymes” are enzymes that recognize specific secondary structures in a nucleic molecule and cleave these structures. The cleavage means of the invention cleave a nucleic acid molecule in response to the formation of cleavage structures; it is not necessary that the cleavage means cleave the cleavage structure at any particular location within the cleavage structure.

The cleavage means may include nuclease activity provided from a variety of sources including the Cleavase enzymes, the FEN-1 endonucleases (including RAD2 and XPG proteins), Taq DNA polymerase and E. coli DNA polymerase I. The cleavage means may include enzymes having 5′ nuclease activity (e.g., Taq DNA polymerase (DNAP), E. coli DNA polymerase I). The cleavage means may also include modified DNA polymerases having 5′ nuclease activity but lacking synthetic activity. Examples of cleavage means suitable for use in the method and kits of the present invention are provided in U.S. Pat. Nos. 5,614,402; 5,795,763; 5,843,669; 6,090; PCT Appln. Nos WO 98/23774; WO 02/070755A2; and WO0190337A2, each of which is herein incorporated by reference it its entirety.

The term “thermostable” when used in reference to an enzyme, such as a 5′ nuclease, indicates that the enzyme is functional or active (i.e., can perform catalysis) at an elevated temperature, i.e., at about 55° C. or higher.

The term “cleavage products” as used herein, refers to products generated by the reaction of a cleavage means with a cleavage structure (i.e., the treatment of a cleavage structure with a cleavage means).

The term “target nucleic acid” refers to a nucleic acid molecule containing a sequence that has at least partial complementarity with at least a probe oligonucleotide and may also have at least partial complementarity with an INVADER oligonucleotide. The target nucleic acid may comprise single- or double-stranded DNA or RNA.

The term “non-target cleavage product” refers to a product of a cleavage reaction that is not derived from the target nucleic acid. As discussed above, in the methods of the present invention, cleavage of the cleavage structure generally occurs within the probe oligonucleotide. The fragments of the probe oligonucleotide generated by this target nucleic acid-dependent cleavage are “non-target cleavage products.”

The term “probe oligonucleotide” refers to an oligonucleotide that interacts with a target nucleic acid to form a cleavage structure in the presence or absence of an INVADER oligonucleotide. When annealed to the target nucleic acid, the probe oligonucleotide and target form a cleavage structure and cleavage occurs within the probe oligonucleotide.

The term “INVADER oligonucleotide” refers to an oligonucleotide that hybridizes to a target nucleic acid at a location near the region of hybridization between a probe and the target nucleic acid, wherein the INVADER oligonucleotide comprises a portion (e.g., a chemical moiety, or nucleotide—whether complementary to that target or not) that overlaps with the region of hybridization between the probe and target. In some embodiments, the INVADER oligonucleotide contains sequences at its 3′ end that are substantially the same as sequences located at the 5′ end of a probe oligonucleotide.

The term “cassette” as used herein refers to an oligonucleotide or combination of oligonucleotides configured to generate a detectable signal in response to cleavage of a probe oligonucleotide in an INVADER assay. In preferred embodiments, the cassette hybridizes to a non-target cleavage product from cleavage of the probe oligonucleotide to form a second invasive cleavage structure, such that the cassette can then be cleaved.

In some embodiments, the cassette is a single oligonucleotide comprising a hairpin portion (i.e., a region wherein one portion of the cassette oligonucleotide hybridizes to a second portion of the same oligonucleotide under reaction conditions, to form a duplex). In other embodiments, a cassette comprises at least two oligonucleotides comprising complementary portions that can form a duplex under reaction conditions. In preferred embodiments, the cassette comprises a label. In particularly preferred embodiments, cassette comprises labeled moieties that produce a fluorescence resonance energy transfer (FRET) effect.

The term “substantially single-stranded” when used in reference to a nucleic acid substrate means that the substrate molecule exists primarily as a single strand of nucleic acid in contrast to a double-stranded substrate which exists as two strands of nucleic acid which are held together by inter-strand base pairing interactions.

As used herein, the phrase “non-amplified oligonucleotide detection assay” refers to a detection assay configured to detect the presence or absence of a particular polymorphism (e.g., SNP, repeat sequence, etc.) in a target sequence (e.g. genomic DNA) that has not been amplified (e.g. by PCR), without creating copies of the target sequence. A “non-amplified oligonucleotide detection assay” may, for example, amplify a signal used to indicate the presence or absence of a particular polymorphism in a target sequence, so long as the target sequence is not copied.

The term “sequence variation” as used herein refers to differences in nucleic acid sequence between two nucleic acids. For example, a wild-type structural gene and a mutant form of this wild-type structural gene may vary in sequence by the presence of single base substitutions and/or deletions or insertions of one or more nucleotides. These two forms of the structural gene are said to vary in sequence from one another. A second mutant form of the structural gene may exist. This second mutant form is said to vary in sequence from both the wild-type gene and the first mutant form of the gene.

The term “liberating” as used herein refers to the release of a nucleic acid fragment from a larger nucleic acid fragment, such as an oligonucleotide, by the action of, for example, a 5′ nuclease such that the released fragment is no longer covalently attached to the remainder of the oligonucleotide.

The term “K_(m)” as used herein refers to the Michaelis-Menten constant for an enzyme and is defined as the concentration of the specific substrate at which a given enzyme yields one-half its maximum velocity in an enzyme catalyzed reaction.

The term “nucleotide analog” as used herein refers to modified or non-naturally occurring nucleotides including but not limited to analogs that have altered stacking interactions such as 7-deaza purines (i.e., 7-deaza-dATP and 7-deaza-dGTP); base analogs with alternative hydrogen bonding configurations (e.g., such as Iso-C and Iso-G and other non-standard base pairs described in U.S. Pat. No. 6,001,983 to S. Benner); non-hydrogen bonding analogs (e.g., non-polar, aromatic nucleoside analogs such as 2,4-difluorotoluene, described by B. A. Schweitzer and E. T. Kool, J. Org. Chem., 1994, 59, 7238-7242, B. A. Schweitzer and E. T. Kool, J. Am. Chem. Soc., 1995, 117, 1863-1872); “universal” bases such as 5-nitroindole and 3-nitropyrrole; and universal purines and pyrimidines (such as “K” and “P” nucleotides, respectively; P. Kong, et al., Nucleic Acids Res., 1989, 17, 10373-10383, P. Kong et al., Nucleic Acids Res., 1992, 20, 5149-5152). Nucleotide analogs include comprise modified forms of deoxyribonucleotides as well as ribonucleotides.

The term “polymorphic locus” is a locus present in a population that shows variation between members of the population (e.g., the most common allele has a frequency of less than 0.95). In contrast, a “monomorphic locus” is a genetic locus at little or no variations seen between members of the population (generally taken to be a locus at which the most common allele exceeds a frequency of 0.95 in the gene pool of the population).

The term “microorganism” as used herein means an organism too small to be observed with the unaided eye and includes, but is not limited to bacteria, virus, protozoans, fungi, and ciliates.

The term “microbial gene sequences” refers to gene sequences derived from a microorganism.

The term “bacteria” refers to any bacterial species including eubacterial and archaebacterial species.

As used herein, the terms “high-risk HPV strains” or “high-risk HPV types” refer to those strains of HPV that have been found in cancers (e.g., carcinomas). These HPV strains include HPV types 16, 18, 30, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 67, 68, 69 and 70.

The term “virus” refers to obligate, ultramicroscopic, intracellular parasites incapable of autonomous replication (i.e., replication requires the use of the host cell's machinery).

The term “multi-drug resistant” or multiple-drug resistant” refers to a microorganism that is resistant to more than one of the antibiotics or antimicrobial agents used in the treatment of said microorganism.

The term “sample” in the present specification and claims is used in its broadest sense. On the one hand it is meant to include a specimen or culture (e.g., microbiological cultures). On the other hand, it is meant to include both biological and environmental samples. A sample may include a specimen of synthetic origin.

Biological samples may be animal, including human, fluid, solid (e.g., stool) or tissue, as well as liquid and solid food and feed products and ingredients such as dairy items, vegetables, meat and meat by-products, and waste. Biological samples may be obtained from all of the various families of domestic animals, as well as feral or wild animals, including, but not limited to, such animals as ungulates, bear, fish, lagamorphs, rodents, etc.

Environmental samples include environmental material such as surface matter, soil, water and industrial samples, as well as samples obtained from food and dairy processing instruments, apparatus, equipment, utensils, disposable and non-disposable items. These examples are not to be construed as limiting the sample types applicable to the present invention.

The term “source of target nucleic acid” refers to any sample that contains nucleic acids (RNA or DNA). Particularly preferred sources of target nucleic acids are biological samples including, but not limited to blood, saliva, cerebral spinal fluid, pleural fluid, milk, lymph, sputum and semen.

An oligonucleotide is said to be present in “excess” relative to another oligonucleotide (or target nucleic acid sequence) if that oligonucleotide is present at a higher molar concentration that the other oligonucleotide (or target nucleic acid sequence). When an oligonucleotide such as a probe oligonucleotide is present in a cleavage reaction in excess relative to the concentration of the complementary target nucleic acid sequence, the reaction may be used to indicate the amount of the target nucleic acid present. Typically, when present in excess, the probe oligonucleotide will be present at least a 100-fold molar excess; typically at least 1 pmole of each probe oligonucleotide would be used when the target nucleic acid sequence was present at about 10 fmoles or less.

A sample “suspected of containing” a first and a second target nucleic acid may contain either, both or neither target nucleic acid molecule.

The term “reactant” is used herein in its broadest sense. The reactant can comprise, for example, an enzymatic reactant, a chemical reactant or light (e.g., ultraviolet light, particularly short wavelength ultraviolet light is known to break oligonucleotide chains). Any agent capable of reacting with an oligonucleotide to either shorten (i.e., cleave) or elongate the oligonucleotide is encompassed within the term “reactant.”

As used herein, the term “purified” or “to purify” refers to the removal of contaminants from a sample. For example, recombinant CLEAVASE nucleases are expressed in bacterial host cells and the nucleases are purified by the removal of host cell proteins; the percent of these recombinant nucleases is thereby increased in the sample.

As used herein the term “portion” when in reference to a protein (as in “a portion of a given protein”) refers to fragments of that protein. The fragments may range in size from four amino acid residues to the entire amino acid sequence minus one amino acid (e.g., 4, 5, 6, . . . , n−1).

The term “nucleic acid sequence” as used herein refers to an oligonucleotide, nucleotide or polynucleotide, and fragments or portions thereof, and to DNA or RNA of genomic or synthetic origin that may be single or double stranded, and represent the sense or antisense strand. Similarly, “amino acid sequence” as used herein refers to peptide or protein sequence.

As used herein, the terms “purified” or “substantially purified” refer to molecules, either nucleic or amino acid sequences, that are removed from their natural environment, isolated or separated, and are at least 60% free, preferably 75% free, and most preferably 90% free from other components with which they are naturally associated. An “isolated polynucleotide” or “isolated oligonucleotide” is therefore a substantially purified polynucleotide.

The term “continuous strand of nucleic acid” as used herein is means a strand of nucleic acid that has a continuous, covalently linked, backbone structure, without nicks or other disruptions. The disposition of the base portion of each nucleotide, whether base-paired, single-stranded or mismatched, is not an element in the definition of a continuous strand. The backbone of the continuous strand is not limited to the ribose-phosphate or deoxyribose-phosphate compositions that are found in naturally occurring, unmodified nucleic acids. A nucleic acid of the present invention may comprise modifications in the structure of the backbone, including but not limited to phosphorothioate residues, phosphonate residues, 2′ substituted ribose residues (e.g., 2′-O-methyl ribose) and alternative sugar (e.g., arabinose) containing residues.

The term “continuous duplex” as used herein refers to a region of double stranded nucleic acid in which there is no disruption in the progression of basepairs within the duplex (i.e., the base pairs along the duplex are not distorted to accommodate a gap, bulge or mismatch with the confines of the region of continuous duplex). As used herein the term refers only to the arrangement of the basepairs within the duplex, without implication of continuity in the backbone portion of the nucleic acid strand. Duplex nucleic acids with uninterrupted basepairing, but with nicks in one or both strands are within the definition of a continuous duplex.

The term “duplex” refers to the state of nucleic acids in which the base portions of the nucleotides on one strand are bound through hydrogen bonding the their complementary bases arrayed on a second strand. The condition of being in a duplex form reflects on the state of the bases of a nucleic acid. By virtue of base pairing, the strands of nucleic acid also generally assume the tertiary structure of a double helix, having a major and a minor groove. The assumption of the helical form is implicit in the act of becoming duplexed.

The term “template” refers to a strand of nucleic acid on which a complementary copy is built from nucleoside triphosphates through the activity of a template-dependent nucleic acid polymerase. Within a duplex the template strand is, by convention, depicted and described as the “bottom” strand. Similarly, the non-template strand is often depicted and described as the “top” strand.

DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a schematic diagram of INVADER oligonucleotides, probe oligonucleotides and FRET cassettes for detecting a two different alleles (e.g., differing by a single nucleotide) in a single reaction.

FIG. 2 shows the results of a temperature optimization experiment carried out in some embodiments of the present invention.

FIGS. 3A and 3B show sequences of detection assay components in some embodiments of the present invention. Underlined portions of the sequence refer to the 5′ arm portion of probe oligonucleotides.

FIG. 4 shows results of HPV strain 16 detection experiments conducted in some embodiments of the present invention.

FIG. 5 shows results of HPV strain 18 detection experiments conducted in some embodiments of the present invention.

FIG. 6 shows HPV strains detected with Invader assay pools A9, A7 and A5/A6.

FIGS. 7A and 7B show sequences of detection assay components in some embodiments of the present invention. Underlined portions of the sequence refer to the 5′ arm portion of probe oligonucleotides.

FIG. 8 shows the quantitation of cervical sample genomic DNA using the Oligreen Quantitation Kit or the Alpha-Actin Invader assays.

FIG. 9 shows detection of HPV and Alpha-Actin in cervical samples conducted in some embodiments of the present invention.

FIGS. 10A-C show sequences of detection assay components in some embodiments of the present invention. Underlined portions of the sequence refer to the 5′ arm portion of probe oligonucleotides.

DESCRIPTION OF THE INVENTION

The present invention provides means for forming a nucleic acid cleavage structure that is dependent upon the presence of a target nucleic acid and cleaving the nucleic acid cleavage structure so as to release distinctive cleavage products. 5′ nuclease activity, for example, is used to cleave the target-dependent cleavage structure and the resulting cleavage products are indicative of the presence of specific target nucleic acid sequences in the sample. When two strands of nucleic acid, or oligonucleotides, both hybridize to a target nucleic acid strand such that they form an overlapping invasive cleavage structure, as described below, invasive cleavage can occur. Through the interaction of a cleavage agent (e.g., a 5′ nuclease) and the upstream oligonucleotide, the cleavage agent can be made to cleave the downstream oligonucleotide at an internal site in such a way that a distinctive fragment is produced. Such embodiments have been termed the INVADER assay (Third Wave Technologies) and are described in U.S. Pat. Nos. 5,846,717, 5,985,557, 5,994,069, 6,001,567, and 6,090,543, WO 97/27214 WO 98/42873, Lyamichev et al., Nat. Biotech., 17:292 (1999), Hall et al., PNAS, USA, 97:8272 (2000), each of which is herein incorporated by reference in their entirety for all purposes).

The INVADER assay detects hybridization of probes to a target by enzymatic cleavage of specific structures by structure specific enzymes (See, INVADER assays, Third Wave Technologies; See e.g., U.S. Pat. Nos. 5,846,717; 6,090,543; 6,001,567; 5,985,557; 6,090,543; 5,994,069; Lyamichev et al., Nat. Biotech., 17:292 (1999), Hall et al., PNAS, USA, 97:8272 (2000), WO97/27214 and WO98/42873, each of which is herein incorporated by reference in their entirety for all purposes).

The INVADER assay detects specific DNA and RNA sequences by using structure-specific enzymes (e.g. FEN endonucleases) to cleave a complex formed by the hybridization of overlapping oligonucleotide probes (See, e.g. FIG. 1). Elevated temperature and an excess of one of the probes enable multiple probes to be cleaved for each target sequence present without temperature cycling. In some embodiments, these cleaved probes then direct cleavage of a second labeled probe. The secondary probe oligonucleotide can be 5′-end labeled with fluorescein that is quenched by an internal dye. Upon cleavage, the de-quenched fluorescein labeled product may be detected using a standard fluorescence plate reader.

The INVADER assay detects specific mutations and SNPs in unamplified, as well as amplified, RNA and DNA including genomic DNA. In the embodiments shown schematically in FIG. 1, the INVADER assay uses two cascading steps (a primary and a secondary reaction) both to generate and then to amplify the target-specific signal. For convenience, the alleles in the following discussion are described as wild-type (WT) and mutant (MT), even though this terminology does not apply to all genetic variations. In the primary reaction (FIG. 1, panel A), the WT primary probe and the INVADER oligonucleotide hybridize in tandem to the target nucleic acid to form an overlapping structure. An unpaired “flap” is included on the 5′ end of the WT primary probe. A structure-specific enzyme (e.g. the CLEAVASE enzyme, Third Wave Technologies) recognizes the overlap and cleaves off the unpaired flap, releasing it as a target-specific product. In the secondary reaction, this cleaved product serves as an INVADER oligonucleotide on the WT fluorescence resonance energy transfer (WT-FRET) probe to again create the structure recognized by the structure specific enzyme (panel A). When the two dyes on a single FRET probe are separated by cleavage (indicated by the arrow in FIG. 1), a detectable fluorescent signal above background fluorescence is produced. Consequently, cleavage of this second structure results in an increase in fluorescence, indicating the presence of the WT allele (or mutant allele if the assay is configured for the mutant allele to generate the detectable signal). In some embodiments, FRET probes having different labels (e.g. resolvable by difference in emission or excitation wavelengths, or resolvable by time-resolved fluorescence detection) are provided for each allele or locus to be detected, such that the different alleles or loci can be detected in a single reaction. In such embodiments, the primary probe sets and the different FRET probes may be combined in a single assay, allowing comparison of the signals from each allele or locus in the same sample.

If the primary probe oligonucleotide and the target nucleotide sequence do not match perfectly at the cleavage site (e.g., as with the MT primary probe and the WT target, FIG. 1, panel B), the overlapped structure does not form and cleavage is suppressed. The structure specific enzyme (e.g., CLEAVASE VIII enzyme, Third Wave Technologies) used cleaves the overlapped structure more efficiently (e.g. at least 340-fold) than the non-overlapping structure, allowing excellent discrimination of the alleles.

The probes turn over without temperature cycling to produce many signals per target (i.e., linear signal amplification). Similarly, each target-specific product can enable the cleavage of many FRET probes.

The primary INVADER assay reaction is directed against the target DNA (or RNA) being detected. The target DNA is the limiting component in the first invasive cleavage, since the INVADER and primary probe are supplied in molar excess. In the second invasive cleavage, it is the released flap that is limiting. When these two cleavage reactions are performed sequentially, the fluorescence signal from the composite reaction accumulates linearly with respect to the target DNA amount.

In certain embodiments, the INVADER assay, or other nucleotide detection assays, are performed with accessible site designed oligonucleotides and/or bridging oligonucleotides. Such methods, procedures and compositions are described in U.S. Pat. No. 6,194,149, WO9850403, and WO0198537, all of which are specifically incorporated by reference in their entireties.

In certain embodiments, the target nucleic acid sequence is amplified prior to detection (e.g. such that synthetic nucleic acid is generated). In some embodiments, the target nucleic acid comprises genomic DNA. In other embodiments, the target nucleic acid comprises synthetic DNA or RNA. In some preferred embodiments, synthetic DNA within a sample is created using a purified polymerase. In some preferred embodiments, creation of synthetic DNA using a purified polymerase comprises the use of PCR. In other preferred embodiments, creation of synthetic DNA using a purified DNA polymerase, suitable for use with the methods of the present invention, comprises use of rolling circle amplification, (e.g., as in U.S. Pat. Nos. 6,210,884, 6,183,960 and 6,235,502, herein incorporated by reference in their entireties). In other preferred embodiments, creation of synthetic DNA comprises copying genomic DNA by priming from a plurality of sites on a genomic DNA sample. In some embodiments, priming from a plurality of sites on a genomic DNA sample comprises using short (e.g., fewer than about 8 nucleotides) oligonucleotide primers. In other embodiments, priming from a plurality of sites on a genomic DNA comprises extension of 3′ ends in nicked, double-stranded genomic DNA (i.e., where a 3′ hydroxyl group has been made available for extension by breakage or cleavage of one strand of a double stranded region of DNA). Some examples of making synthetic DNA using a purified polymerase on nicked genomic DNAs, suitable for use with the methods and compositions of the present invention, are provided in U.S. Pat. Nos. 6,117,634, issued Sep. 12, 2000, and U.S. Pat. No. 6,197,557, issued Mar. 6, 2001, and in PCT application WO 98/39485, each incorporated by reference herein in their entireties for all purposes.

In some embodiments, the present invention provides methods for detecting a target sequence, comprising: providing a) a sample containing DNA amplified by extension of 3′ ends in nicked double-stranded genomic DNA, said genomic DNA suspected of containing said target sequence; b) oligonucleotides capable of forming an invasive cleavage structure in the presence of said target sequence; and c) exposing the sample to the oligonucleotides and the agent. In some embodiments, the agent comprises a cleavage agent. In some particularly preferred embodiments, the method of the invention further comprises the step of detecting said cleavage product.

In some preferred embodiments, the exposing of the sample to the oligonucleotides and the agent comprises exposing the sample to the oligonucleotides and the agent under conditions wherein an invasive cleavage structure is formed between said target sequence and said oligonucleotides if said target sequence is present in said sample, wherein said invasive cleavage structure is cleaved by said cleavage agent to form a cleavage product.

In some particularly preferred embodiments, the target sequence comprises a first region and a second region, said second region downstream of and contiguous to said first region, and said oligonucleotides comprise first and second oligonucleotides, said wherein at least a portion of said first oligonucleotide is completely complementary to said first portion of said target sequence and wherein said second oligonucleotide comprises a 3′ portion and a 5′ portion, wherein said 5′ portion is completely complementary to said second portion of said target nucleic acid.

In other embodiments, synthetic DNA suitable for use with the methods and compositions of the present invention is made using a purified polymerase on multiply-primed genomic DNA, as provided, e.g., in U.S. Pat. Nos. 6,291,187, and 6,323,009, and in PCT applications WO 01/88190 and WO 02/00934, each herein incorporated by reference in their entireties for all purposes. In these embodiments, amplification of DNA such as genomic DNA is accomplished using a DNA polymerase, such as the highly processive Φ29 polymerase (as described, e.g., in U.S. Pat. Nos. 5,198,543 and 5,001,050, each herein incorporated by reference in their entireties for all purposes) in combination with exonuclease-resistant random primers, such as hexamers.

In some embodiments, the present invention provides methods for detecting a target sequence, comprising: providing a) a sample containing DNA amplified by extension of multiple primers on genomic DNA, said genomic DNA suspected of containing said target sequence; b) oligonucleotides capable of forming an invasive cleavage structure in the presence of said target sequence; and c) exposing the sample to the oligonucleotides and the agent. In some embodiments, the agent comprises a cleavage agent. In some preferred embodiments, said primers are random primers. In particularly preferred embodiments, said primers are exonuclease resistant. In some particularly preferred embodiments, the method of the invention further comprises the step of detecting said cleavage product.

In some preferred embodiments, the exposing of the sample to the oligonucleotides and the agent comprises exposing the sample to the oligonucleotides and the agent under conditions wherein an invasive cleavage structure is formed between said target sequence and said oligonucleotides if said target sequence is present in said sample, wherein said invasive cleavage structure is cleaved by said cleavage agent to form a cleavage product.

In some preferred embodiments, the exposing of the sample to the oligonucleotides and the agent comprises exposing the sample to the oligonucleotides and the agent under conditions wherein an invasive cleavage structure is formed between said target sequence and said oligonucleotides if said target sequence is present in said sample, wherein said invasive cleavage structure is cleaved by said cleavage agent to form a cleavage product.

In some particularly preferred embodiments, the target sequence comprises a first region and a second region, said second region downstream of and contiguous to said first region, and said oligonucleotides comprise first and second oligonucleotides, said wherein at least a portion of said first oligonucleotide is completely complementary to said first portion of said target sequence and wherein said second oligonucleotide comprises a 3′ portion and a 5′ portion, wherein said 5′ portion is completely complementary to said second portion of said target nucleic acid.

In certain embodiments, the present invention provides kits for assaying a pooled sample (e.g., a pooled blood sample) using INVADER detection reagents (e.g. primary probe, INVADER probe, and FRET cassette). In preferred embodiments, the kit further comprises instructions on how to perform the INVADER assay and specifically how to apply the INVADER detection assay to pooled samples from many individuals, or to “pooled” samples from many cells (e.g. from a biopsy sample) from a single subject.

The present invention further provides assays in which the target nucleic acid is reused or recycled during multiple rounds of hybridization with oligonucleotide probes and cleavage of the probes without the need to use temperature cycling (i.e., for periodic denaturation of target nucleic acid strands) or nucleic acid synthesis (i.e., for the polymerization-based displacement of target or probe nucleic acid strands). When a cleavage reaction is run under conditions in which the probes are continuously replaced on the target strand (e.g. through probe-probe displacement or through an equilibrium between probe/target association and disassociation, or through a combination comprising these mechanisms, (The kinetics of oligonucleotide replacement. Luis P. Reynaldo, Alexander V. Vologodskii, Bruce P. Neri and Victor I. Lyamichev. J. Mol. Biol. 97: 511-520 (2000)), multiple probes can hybridize to the same target, allowing multiple cleavages, and the generation of multiple cleavage products.

In some embodiments, the detection assays of the present invention are designed to detect one or more HPV sequences (See, e.g., Example 5). In some embodiments, multiple HPV sequences are detected in a single reaction (See, e.g., Example 5, FIG. 9, reactions 10-658, 10-662, 10-677 and 10-682). In some preferred embodiments, a single oligonucleotide used in the detection assays is configured to hybridize to two or more HPV sequences such that multiple HPV sequences can be detected with a single set of detection assay reagents (See, e.g., Example 5, FIG. 9). In some embodiments, the oligonucleotides used in the detection assay are perfectly complementary to the intended HPV target sequence. In other embodiments, the oligonucleotides contain one or more mismatches to the HPV target sequence of interest. Mismatches find multiple uses, including, but not limited to, the ability to reduce hybridization efficiency (which may be desired in some detection assay formats), the ability to add degeneracy (e.g., to detect two or more strains or variants), and the ability to compensate for sequence variation that may be in a sample. In some embodiments, where variation at a particular nucleotide position is identified in some members of a tested population, multiple oligonucleotides are provides that differ in sequence at the position so that each variant within the population is detected. Exemplary detection assay components for use in invasive cleavage assays are provided in the Example section below for certain preferred strains of HPV.

EXAMPLES

The following examples are provided in order to demonstrate and further illustrate certain preferred embodiments and aspects of the present invention and are not to be construed as limiting the scope thereof.

In the experimental disclosure which follows, the following abbreviations apply: N (normal); M (molar); mM (millimolar); μM (micromolar); mol (moles); mmol (millimoles); μmol (micromoles); nmol (nanomoles); pmol (picomoles); g (grams); mg (milligrams); μg (micrograms); ng (nanograms); l or L (liters); ml (milliliters); μl (microliters); cm (centimeters); mm (millimeters); μm (micrometers); nm (nanometers); DS (dextran sulfate); ° C. (degrees Centigrade); and Sigma (Sigma Chemical Co., St. Louis, Mo.).

Example 1 Design of Oligonucleotides to Detect Multiple HPV Strains

The objective of these experiments was to arrive at oligonucleotide designs suitable for use in INVADER assays comprising multiple target HPV strains. As a first step, HPV DNA sequences were obtained from Genbank and aligned using SEQ WEB GAP and PRETTY programs (Accelrys, San Diego, Calif.). Only those regions of HPV that are reported to remain intact following chromosomal integration were analyzed to permit the assays to detect both integrated and non-integrated HPV sequences. Regions of suitable sequence conservation were chosen for select groups of strains. In this example, areas within the LCR, E6, and E7 genes were found to have considerable homology between HPV 18 and 59.

Candidate probe oligonucleotides were designed by searching for stretches of sequence comprising a limited number of mismatches between the two targets in either pair. Designs were generated to several sequences on either the sense or antisense strands. Suitable INVADER oligonucleotides were designed to accompany the respective probe oligonucleotide candidates. Initial INVADER oligonucleotide designs were selected to associate with only a single target, e.g. HPV 18, HPV 45, or HPV 59; subsequent designs hybridize to more than one HPV strain. Candidate probe sets were then evaluated for two types of performance criteria: (1) signal generation at the chosen reaction temperature and (2) limit of detection, i.e. signal over background ratios at low levels of target DNA. Probe sets meeting desired performance cut-offs, in this case, optimal signal generation at 63° C. and LOD of ≦1000 copies of HPV DNA, were then selected for further evaluation.

Temperature Optimization

INVADER assays were performed in 96 well MJ Skirted microtiter plates. Plates were incubated using either an MJ Research PTC 100 Thermocycler or a ThermoHybaid PCR Express (Molecular Biology Instrumentation, Needham Heights, Mass.) and read with an Applied Biosystems CYTOFLUOR® 4000 series multiwell plate reader.

INVADER assays to determine temperature optima of probe sets were set up by preparing primary and secondary reaction master mixes. In these experiments, two different INVADER oligonucleotides were tested in combination with a single probe oligonucleotide in each reaction. For example, in experiments designed to test probe sets for HPV 18 and 59, INVADER oligonucleotides for both HPV 18 and HPV 59 were included in each reaction along with a single probe oligonucleotide designed to associate with both strains of HPV. These reaction mixtures were tested separately on plasmid DNA comprising a portion of the HPV 18 (18c1) sequence (ATCC Catalog Number: 45152D) and a synthetic target comprising a portion of the HPV 59 sequence (SEQ ID NO: 42). Similarly, in experiments designed to detect HPV 45 and 59, INVADER oligonucleotides for both strains were included in each reaction along with the corresponding probe oligonucleotide and appropriate controls.

Master mixes containing primary reaction components were assembled for each set of temperature optimization reactions as follows. Reactions were carried out in parallel in microtiter plates.

Primary Mix (PM) Stock Final Total Reagent Conc. Conc. # Rxns Vol/Rxn Vol Invader Oligo 10 0.05 120 0.10 12 1 (μM) Invader Oligo 10 0.05 0.10 12 2 (μM) Primary 10 0.5 1.00 120 Probe (μM) MOPS (mM) 400 10 0.50 60 CLEAVASE × enzyme 50 2.5 1.00 120 (ng/μl) MgCl₂ (mM) 250 12.5 1.00 120 Distilled 0 0 0.30 36 Water 4.00 μl/rxn

Aliquots of 15 μl of each target at a concentration of 20 fM were placed in the appropriate wells of a microtiter plate and were overlaid with 20 μl of mineral oil; 20 μl of 10 ng/μl tRNA were used for the no target control reactions. All reactions were run in duplicate. The targets were heat denatured at 95° C. for 5 minutes, cooled to 20° C., and then aliquots of 4 μl of the primary mix were added to each well. The microtiter plates were incubated for 2 hours in a ThermoHybaid thermocycler with a gradient heat block over a span of 10 degrees (i.e. reactions were run at 58, 58.3, 58.9, 59.8, 60.9, 62.2, 63.5, 64.9, 66.4, 67.3, 67.8, 68.1° C.) and then returned to 20° C.

A secondary master mix (SM) was assembled as follows.

Secondary Mix (SM) Stock Final Reagent Conc. Conc. Vol/Rxn Total Vol FRET Cassette  10 0.25 0.50 62.50 Arm 1 FAM SEQ ID NO: 63 (μM) MOPS (mM) 400 0.91 0.05 5.68 Water — — 2.45 306.82 3 μl/rxn

Aliquots of 3 μl of secondary mix were then added to each well, and the plate was incubated at 63° C. for 10 minutes and then cooled to 4° C. prior to scanning in a CYTOFLUOR 4000 fluorescence plate reader (Applied Biosystems, Foster City, Calif.). The settings used were: 485/20 nm excitation/bandwidth and 530/25 nm emission/bandwidth for FAM dye detection. Unlike typical biplex INVADER reactions, because these assays include only a single probe molecule, only the single corresponding FRET cassette is required. The instrument gain was set for each dye so that the No Target Blank produced between 50-150 Relative Fluorescence Units (RFUs).

Because the optimal gain setting can vary between instruments, gain is adjusted as needed to give the best signal/background ratio (sample raw signal divided by the No Target Control signal) or No Target Control sample readings of 100 RFUs. Fluorescence microplate readers that use a xenon lamp source generally produce higher RFUs. For directly reading the microplates, the probe height of, and how the plate is positioned in, the fluorescence microplate reader may need to be adjusted according to the manufacturer's recommendations.

The raw data that is generated by the device/instrument is used to measure the assay performance (real-time or endpoint mode). The equations below provide how FOZ (Fold Over Zero), and other values are calculated. NTC in the equations below represents the signal from the No Target Control.

FOZ or Signal/No Target

-   -   FOZ_(Dye1)=(RawSignal_(Dye1)/NTC_(Dye1))

Candidate probe sets were selected based on the temperature profiles generated in these experiments. In particular, desirable probe sets exhibit temperature profiles on the two targets (e.g. HPV 18 and 59) tested together that exhibit similar trends with respect to increase in temperature, typically a bell shaped curve with its peak at the chosen reaction temperature, in this case 63° C. An additional desirable feature is that the peak not be precipitously lower plus or minus 1 or 2 degrees from 63° C. Fewer than 30% of the candidate probe sets yielded suitable temperature profiles.

In order to unify reaction conditions at a single reaction temperature, probe designs that gave rise to similar trends in response to temperature were chosen for further design optimization. Redesigned probes in which probe length was altered were tested. FIG. 2 shows the results of a temperature optimization experiment carried out with probe T3e1b (SEQ ID NO:39) and INVADER oligonucleotides designed to detect HPV 18 (T3e4i) (SEQ ID NO:40) and HPV 59 (T3e6i) (SEQ ID NO:41), respectively, on both the HPV 18 plasmid and HPV 59 (T3rT59) synthetic target (SEQ ID NO:42).

Similar temperature optimization and redesign procedures were carried out for all of the oligonucleotides presented in FIGS. 3 and 7.

Limit of Detection (LOD) Analysis

In addition to optimizing for temperature profiles that follow the same general trends in response to temperature and do not present steep slopes in the immediate vicinity of the target reaction temperature, it is also desirable to optimize probe sets for analytical sensitivity or limit of detection (LOD). Measuring LOD is accomplished by conducting INVADER assays at a single reaction temperature while varying target concentration.

Reactions to determine LOD of temperature optimized probe sets were set up as follows. A dilution series of target DNAs (HPV 18 plasmid and synthetic target SEQ ID NO: 42) was made in 10 ng/μl tRNA in dH₂O; in the example presented here, target amounts per assay ranged from 125 copies/r×n to 8000 copies/r×n, doubling in each successive reaction. Aliquots of 15 μl of diluted target or 10 ng/μl tRNA in dH₂O for the no target controls were placed in appropriate wells of a microtiter plate and overlaid with 20 μl of mineral oil. All reactions were run in quadruplicate. A master mix (MM) was made containing buffer, CLEAVASE X enzyme, MgCl₂, both INVADER oligonucleotides (SEQ ID NOs: 40-41), primary probe T3e1b (SEQ ID NO: 39) and FRET cassette oligonucleotides (SEQ ID NO: 63) as below.

Master Mix (MM): no. 125 rxns Stock Final Vol/ Reagent Conc. Conc. Rxn Total Vol FRET Cassette (μM) 10 0.25 0.5 62.5 MOPS (mM) 400 10 0.5 62.5 CLEAVASE × enzyme 50 2.5 1 125 (ng/μl) MgCl2 (mM) 250 12.5 1 125 Invader oligo 1 10 0.05 0.1 12.5 (μM) Invader oligo 2 10 0.05 0.1 12.5 (uM) Primary Probe 10 0.5 1 125 (μM) water N/A N/A 0.8 100 total volume 5 625

Microtiter plates were covered and incubated at 95° C. for 5 minutes to denature the targets and then cooled to 20° C. Aliquots of 5 μl of master mix were added and the reactions heated to 63° C. for 4 hours. Upon completion, plates were removed to the CYTOFLUOR plate reader and analyzed as described above. Representative results are presented FIG. 2. These results demonstrate that the designs tested in this experiment are suitable for the detection of as few as 250 copies of the corresponding HPV 18 and 59 sequences.

Example 2 Design of Oligonucleotides to Detect HPV 16

Candidate oligonucleotide sets having a primary probe and an INVADER oligonucleotide were designed to detect regions in both HPV 16 and HPV 31 using the procedures described in the preceding examples. Designs were directed to the E7 gene of HPV. As in Example 1, different INVADER oligonucleotide sequences were tested in combination with a single probe sequence to find a probe set with optimal performance characteristics at the desired reaction temperature (63° C.) and in terms of limit of detection (FOZ). Both temperature optimization experiments and LOD (FOZ) experiments were conducted as described above using 15 μl of a 20 fM stock solution of HPV 16 plasmid (ATCC Catalog Number: 45113D). A total of 24 different INVADER oligonucleotides were tested with SEQ ID NO: 1 (Alg3p); of these, one was chosen for use in assays to detect HPV 16: SEQ ID NO: 2 (Alg10ci), based on its temperature optimization profile and FOZ.

Co-Detection of HPV 16 and a Human Genomic Internal Control Sequence

In some applications, it is desirable to co-detect an internal control sequence, for example in order to determine whether or not there are sample inhibition effects or operator errors. Oligonucleotide sets were designed to detect three different human genomic sequences and were tested in three different biplexed INVADER assays in combination with SEQ ID NOs: 1 and 2 to detect the HPV 16 plasmid. The human genomic regions were alpha actin (Genbank accession number NM_(—)001100), the 3′ untranslated region (UTR) of CFTR (Genbank accession number NM_(—)000492), and hIGF (Genbank accession number AY260957). The oligonucleotides used for these designs were developed previously and optimized as described in the previous examples and were as follows: alpha actin probe SEQ ID NO: 64, INVADER oligo, SEQ ID NO: 65, FRET cassette 68; 3′ UTR CFTR probe SEQ ID NO: 66, INVADER oligo SEQ ID NO: 67, FRET cassette SEQ ID NO: 68; hIGF probe SEQ ID NO: 69, INVADER oligo SEQ ID NO: 70, FRET cassette SEQ ID NO: 71.

A standard curve was generated using different amounts of HPV 16 plasmid against a constant amount of human genomic DNA. Reactions containing 0, 250, 500, 1000, 2500, 5000, 10,000, or 20,000 copies of the HPV 16 plasmid and either 100 ng (for hIGF and CFTR) or 250 ng (for alpha actin) human genomic DNA. DNA was isolated using the Gentra PUREGENE® Autopure LS system (Gentra, Inc., Minneapolis, Minn.) or manual preparation methods. All other reaction components and detection were as described in the previous examples except that a second FRET oligo was used in each case (for hIGF, SEQ ID NO: 71, red dye; for 3′ UTR of CFTR and alpha actin, SEQ ID NO: 68, red dye). The results are presented in FIG. 4 and indicate that all of the human genomic sequences tested were suitable for biplex detection in combination with varying levels of HPV 16 plasmid DNA. Furthermore, these experiments demonstrate that there is no apparent cross reactivity between the probe sets designed to detect HPV 16 and those designed to detect the human genomic sequences, as evidenced by both the unchanged signal generated using the IC probes in the presence of variable amounts of HPV 16 DNA as well as by the lack of detectable signal generated using the HPV 16 probes in the absence of HPV 16 plasmid DNA.

Example 3 Effects of Genomic DNA on Detection of HPV 18

Experiments were carried out to assess the effect of exogenous human genomic DNA on detection of HPV 18. INVADER reactions were set up as follows. Serial dilutions of a synthetic HPV 18 target B1T18 (SEQ ID NO: 72) were made to result in numbers of target molecules as indicated in the X-axis of FIG. 5 when 15 μl were pipetted into the appropriate wells of a microtiter plate. A second set of serial dilutions was made incorporating human genomic DNA, purified as described in Example 2, into each dilution such that each reaction contained 1 μg of human genomic DNA. No target controls contained 15 μl of 10 ng/μl tRNA in distilled water. All reactions were run in duplicate. The target aliquots were overlaid with 20 μl mineral oil and denatured at 95° C. for 5 minutes then chilled to 20° C. A master mix containing INVADER reaction components was made as follows.

Stock Final # of Volume/ Total Reagent Conc. Conc. reactions reaction volume INVADER oligo mixture 1 0.05 10 1 10 (SEQ ID NO: 73, 74, and 75) (μM) Primary probe (SEQ ID 10 0.5 1 10 NO: 76) B1b3 (μM) FRET Cassette (SEQ ID 10 0.25 0.5 5 NO: 63) (μM) MOPS (mM) 400 10 0.5 5 CLEAVASE × enzyme 50 2.5 1 10 (ng/μl) MgCl₂ (mM) 250 12.5 1 10 Total volume 5 50 Aliquots of 5 μl of the master mix were added to each well. Reactions were incubated at 62° C. for 4 hours and then read in the CYTOFLUOR as described above.

The results are presented in FIG. 5 and demonstrate that the presence of 1 μg of human genomic DNA does not exert a significant inhibitory effect on the INVADER assay designed to detect HPV 18 sequences.

Example 4 Simultaneous Detection of Multiple HPV Strains in a Single Pooled Reaction

In some situations, it may prove desirable to combine detection of many HPV strains in a single reaction vessel. For example, it may be desired to detect all high-risk HPV strains or all low-risk strains in a single reaction mixture. In some cases, the output of a pooled reaction is a qualitative answer such as a positive result, indicating the presence of one or more HPV strains, or a negative result, indicating the absence of HPV.

Preferred oligonucleotide designs for pooling multiple INVADER reactions in a single well may possess the following characteristics:

-   -   The oligonucleotides do not interact with one another to promote         excessive signal generation in the absence of a specific target.         Background in the INVADER assay may result from fragments of         certain oligonucleotides that are an intrinsic component of some         oligo synthesis mixtures. However, it is also possible for         groups of different oligonucleotides to assume structures that         are recognized and cleaved during the INVADER assay in the         absence of target.     -   The oligonucleotides do not interact with one another to         interfere significantly with signal generation in the presence         of a specific target.     -   Performance of a given oligonucleotide set is comparable when         tested in the pooled mixture and individually.

Pooled assays are created by combining probe and INVADER oligonucleotides in subcombinations and then assessing performance on each target by comparing signal generation and FOZ of the oligonucleotides in the pool to detection of that target in reactions containing only the probe and INVADER oligonucleotides designed to detect it. In the event that a given oligonucleotide set is adversely affected by combination with other oligo sets in a single reaction vessel, e.g. generates excessive background or fails to generate the expected levels of target-specific signal, in some cases it is possible to swap in an alternative oligonucleotide set useful for determining the presence of the same HPV strain. In other cases, it is possible to merely choose a different 5′ arm for a particular probe oligonucleotide to reduce non-specific background generation or signal inhibition. In some cases, it is possible to detect the alternative strand of a particular target sequence, thereby altering the composition of the oligonucleotides and making them suitable for detection of the target in a pooled assay. In each case, the measure of a successfully performing assay is yield of statistically significant signal over background (FOZ) in the presence of the desired targets, e.g. ≧1.15 with t-test from neighbor <0.05.

Ultimately, candidate oligonucleotide designs are pooled in various combinations and tested against a sample containing purified HPV DNA or partial HPV sequences. Optimally, samples of all HPV strains being tested are evaluated individually with the pooled oligonucleotide sets to confirm that target-specific signal is generated for each desired strain. Similarly, HPV negative samples or samples containing strains of HPV not desired to be tested (e.g. low risk strains, HPV 1, or other non-cervical strains) are also tested against the pools to confirm that they do not generate statistically significant FOZ.

Example 5 Detection of Multiple HPV Strains in Cervical Samples

The methods and compositions of the present invention were used, as described in Example 4, to detect multiple strains of HPV in cervical samples.

INVADER Oligonucleotide Designs

The INVADER assay was designed to detect high-risk HPV strains including 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 67, 68, and 70. Probe sets were combined into three pools based on HPV genetic phylogeny. Probe sets (e.g., probe and INVADER oligonucleotides) were designed to hybridize to at least 2 different target regions for each HPV strain to accommodate for sequence polymorphisms and increase analytical sensitivity (See, e.g., FIG. 6). Multiple HPV strains are detected by each of the three pools using the INVADER assay (See, e.g., FIG. 6). Probe and INVADER oligonucleotide sequences are listed in FIG. 7. The probe and INVADER oligonucleotide sequences in FIG. 10 may also be used. An internal control assay (alpha-actin) is included in each pool to measure the relative amount of genomic DNA levels in the samples and to provide a semi-quantitative method for HPV titer. The HPV specific probes in the A7 and A9 pools contained arm 1 (CGCGCCGAGG; SEQ ID NOS: 85, 88, 91, 94, 97, 101, 105, 108, 110, and 114) and utilized the corresponding FAM FRET cassette (Fam-TCT-Z28-AGCCGGTTTTCCGGCTGAGACCTCGGCGCG-hex, SEQ ID NO: 119). The HPV specific probes in the A5/A6 pool contained arm AH9 (GGCAGTCTGGGAGT, SEQ ID NO: 77, 79, 81, and 83) and utilized the FAM FRET cassette (Fam-TCT-Z28-AGCCGGTTTTCCGGCTGAGAACTCCCAGACTGCC-hex, SEQ ID NO: 120). The alpha-actin assay contained arm 3 (ACGGACGCGGAG; SEQ ID NO: 117) and utilized the RED FRET cassette (Red-TCT-Z28-TCGGCCTTTTGGCCGAGAGACTCCGCGTCCGT-hex, SEQ ID NO. 121).

INVADER Assay Reagents and Methods

Preparation of genomic DNA from cervical samples: DNA was isolated from cervical samples obtained from a clinical laboratory using PUREGENE (Gentra Systems) DNA Purification Kit. The extraction procedure was modified to increase DNA yield and purity from this type of specimen using the following procedure:

-   -   1. Remove 1 ml of cervical specimen and transfer to 1.5 ml tube.     -   2. Centrifuge cells at 16000 g for 5 min.     -   3. Remove supernatant and resuspend pellet in Cell Lysis         Solution     -   4. Heat lysates at 99° C. for 10 minutes. Let cool to room         temperature.     -   5. Add proteinase K and incubate at 55 for 1 hour.     -   6. Add 100 μl of protein precipitation solution.     -   7. Vortex samples vigorously for 20 seconds. Place on ice for 10         minutes.     -   8. Centrifuge at 16000 g for 5 min.     -   9. Pour off the supernatant into a clean 1.5 ml tube containing         1.5 μl of glycogen (20 mg/ml)     -   10. Add 300 μl of 100% isopropanol.     -   11. Mix the sample gently by inverting 50 times.     -   12. Centrifuge at 16000 g for 5 min.     -   13. Pour off the supernatant and drain tube on clean absorbent         paper.     -   14. Add 500 μl of 70% ethanol and invert the tube to wash the         DNA pellet.     -   15. Centrifuge at 16000 g for 2 min. Carefully pour off         supernatant.     -   16. Invert and drain the tube on a clean absorbant paper and         allow to air dry for 10-15 min.     -   17. Add 100 μl of distilled water to the pellet.     -   18. Let sit at room temperature overnight.

10 μl aliquots of each genomic DNA sample or no target control (10 ng/μl tRNA) were added to a 96 well microtiter plate. Samples were overlaid with 20 μl mineral oil, denatured at 99° C. for 10 minutes and then cooled to 63° C. A 10 μl aliquot of the INVADER reaction mix was then added to each well and mixed by pipetting. An example of what is contained in the INVADER assay reaction mix is shown below.

Amount per Final concentrations Component reaction (in 20 μl reaction) MgCl2 (70 mM) 4 μl   14 mM MgCl₂ HPV Pooled Primary probes 4 μl  0.5 μM of each probe and INVADER oligos/FAM 0.05 μM of each Invader oligo FRET/MOPS 0.25 μM FRET cassette Stock conc.   10 mM MOPS 2.5 μM of each probe 0.25 μM of each Invader oligo 1.25 μM of FRET cassette 40 mM MOPS Alpha Actin Primary probe/ 1 μl 0.25 μM probe INVADER oligo/RED 0.05 μM Invader oligo FRET/MOPS Stock conc. 0.25 μM FRET cassette 5 μM probe   10 mM MOPS 1 μM Invader oligo 5 μM of FRET 40 mM MOPS CLEAVASE × enzyme 1 μl   2 ng/μl (40 ng/μl) in CLEAVASE dilution buffer

INVADER Assay Reactions

Reactions were incubated at 63° C. for 4 hours and then cooled to 4° C. prior to scanning in a CYTOFLUOR 4000 fluorescence plate reader (Applied Biosystems, Foster City, Calif.). The settings used were: 485/20 nm excitation/bandwidth and 530/25 nm emission/bandwidth for FAM dye detection, and 560/20 nm excitation/bandwidth and 620/40 nm emission/bandwidth for RED dye detection. The instrument gain was set for each dye so that the No Target Blank produced between 100-250 Relative Fluorescence Units (RFUs). Microplates were also read in the Genios FL Plate reader (Tecan, Research Triangle Park, N.C.). The settings used were: 485/535 nm excitation/emission for FAM dye detection, and 560/612 nm excitation/emission for RED dye detection. The instrument gain was set for each dye so that the No Target Blank produced between 1000-2000 Relative Fluorescence Units (RFUs). Because the optimal gain setting can vary between instruments, the gain was adjusted to provide the best signal/background ratio (e.g., sample raw signal divided by the No Target Control signal) or No Target Control sample readings. For directly reading the microplates, the probe height of the microplate reader and the positioning of the plate was adjusted according to the manufacturer's recommendations.

The fluorescent signal from the Fam dye and the Red dye for the samples and No Target Control (NTC) was used to calculate fold over zero (FOZ) values as shown below.

-   -   FOZ_(Fam) dye=(RawSignal_(Fam)/NTC_(Fam))     -   FOZ_(Red)=(RawSignal_(Red)/NTC_(Red))     -   The Fam FOZ corresponds to the signal from the HPV assays, and         the RED FOZ corresponds to the alpha-actin signal (See, e.g.,         FIG. 9).

Results of INVADER Assays for Detection HPV in Cervical Specimens

Quantification of DNA concentration in cervical samples may be achieved using various methods. For example, DNA concentration can be measured using the OliGreen ssDNA Quantitation kit (Molecular probes) or the alpha-actin INVADER assay (See, e.g., FIG. 8). To determine the amount of DNA present in each sample using the INVADER Assay, a control genomic DNA sample was serially diluted to generate a standard curve. The alpha-actin INVADER assay standard curve was used to determine the amount of DNA present in each sample using a linear regression analysis. Both methods are useful for determining concentrations of DNA in cervical samples. Since the signal from the alpha-actin INVADER assay can be detected in the same well as the HPV INVADER assays, a separate quantitation step by OliGreen or measuring absorbance at 260 nm is not required.

The INVADER assay was used to detect the presence or absence of HPV (e.g., high-risk HPV strains) in cervical samples (See, e.g., FIG. 9). Each sample was tested in three separate wells of a microtiter plate containing either the A5/A6, A7 or A9 INVADER reaction mix. All wells contained the alpha-actin oligonucleotides and FRET cassette. Samples were considered to be HPV positive if the FAM FOZ values were greater than 3, HPV negative if the FAM FOZ values were less than 2, and equivocal if the FAM FOZ values were between 2 and 3. Of the 45 cervical samples tested, there were 21 positive samples, 23 negative samples, and 1 equivocal sample. Four of the samples were determined, using the methods of the present invention, to be co-infected with multiple HPV strains (See, e.g., FIG. 9, samples 10-658, 10-662, 10-677 and 10-682).

All publications and patents mentioned in the above specification are herein incorporated by reference as if expressly set forth herein. Various modifications and variations of the described assays of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention that are obvious to those skilled in relevant fields are intended to be within the scope of the following claims. 

1. A method for detecting the presence or absence of a HPV target nucleic acid in a sample, wherein said HPV target nucleic acid is from one or more strains in a set of strains of HPV, comprising: a) providing: i) a sample suspected of containing a HPV target nucleic acid; ii) a composition comprising a mixture of oligonucleotide probe sets, wherein: A) each of said oligonucleotide probe sets comprises a first oligonucleotide and a second oligonucleotide that in combination form an invasive cleavage structure with target nucleic acid from at least two different strains of HPV in said set of strains of HPV wherein said mixture of oligonucleotide probe sets comprises the group of oligonucleotides consisting of SEQ ID NOS: 109-113, 115, 116, 160, 161, 163, 166, 173, 175, 177 and 180, B) each of said oligonucleotide probe sets forms an invasive cleavage structure with target nucleic acid from fewer than all of the different strains in said set of strains of HPV, and C) at least two of said probe sets are configured to form an invasive cleavage structure with target nucleic acid from each different strain of HPV in said set of strains of HPV; and iii) a 5′ nuclease; b) exposing said sample to said composition under reaction conditions in which, if an HPV target nucleic acid from one or more strains in said set of strains is present, at least two of said oligonucleotide probe sets hybridize to said HPV target nucleic acid to form invasive cleavage structures, and in which said at least two invasive cleavage structures are cleaved with said 5′ nuclease; and c) detecting cleavage of said invasive cleavage structures, wherein detection of cleavage of said invasive cleavage structures is indicative of the presence of HPV target nucleic acid from at least one strain of said set of strains of HPV in said sample.
 2. The method of claim 1, wherein said HPV target nucleic acid is from strain 16, 16Ty2, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 58iso, 59, 66, 67, 68, 68var, 69, 70, or
 82. 3. The method of claim 1, wherein said mixture detects HPV strains 51, 56, and
 66. 4. The method of claim 1, wherein said mixture detects HPV strains 39, 68, 68var, 45, 59 and
 18. 5. The method of claim 1, wherein said mixture detects HPV strains 33, 52, 58, 31, 35 and
 16. 6. The method of claim 1, wherein said 5′ nuclease is a FEN-1.
 7. The method of claim 1, wherein said 5′ nuclease is thermostable.
 8. The method of claim 1, wherein said HPV target nucleic acid is amplified prior to said exposure step.
 9. The method of claim 1, wherein said mixture of oligonucleotide probe sets further comprises a pair of oligonucleotide primers configured to amplify a sequence contained in said HPV target nucleic acid in a polymerase chain reaction.
 10. The method of claim 1, wherein said HPV target nucleic acid is a synthetic nucleic acid.
 11. The method of claim 1, wherein said HPV target nucleic acid is genomic HPV nucleic acid.
 12. The method of claim 1, wherein two or more mixtures of oligonucleotide probes are used together to detect said HPV target nucleic acid.
 13. The method of claim 1, wherein two or more of said mixtures of oligonucleotide probes are used together to detect all high-risk HPV strains.
 14. The method of claim 1, wherein said sample is from the group consisting of cervical cells, cervical secretions, epithelial cells, respiratory secretions, urethral cells, cells of the anogenital region, urine, saliva and biopsy tissue.
 15. The method of claim 1, wherein said second oligonucleotides comprise a detectable label.
 16. The method of claim 1, wherein cleavage of said invasive cleavage structures cleaves said second oligonucleotide to produce a cleaved 5′ region of said second oligonucleotide, wherein said providing step further comprises providing an oligonucleotide FRET cassette, wherein said oligonucleotide FRET cassette comprises a set of interactive labels, wherein said oligonucleotide FRET cassette is configured to form a second invasive cleavage structure with said cleaved 5′ region of said second oligonucleotide.
 17. The method of claim 16, wherein said cleaving further comprises cleaving said second invasive cleavage structure.
 18. The method of claim 16, wherein said detecting comprises detecting and/or measuring a signal produced from one or more members of a set of interactive labels.
 19. The method of claim 3, wherein said mixture of oligonucleotide probe sets comprises the group of oligonucleotides consisting of SEQ ID NOS. 47, 51, 52, 79, and
 80. 20. The method of claim 4, wherein said mixture of oligonucleotide probe sets comprises the group of oligonucleotides consisting of SEQ ID NOS. 37, 38, 94, 95, 127, 129 and
 142. 